PDB entry 6pmd

View 6pmd on RCSB PDB site
Description: structure of clpp from staphylococcus aureus in complex with acyldepsipeptide
Deposited on 2019-07-01, released 2019-11-06
The last revision was dated 2019-12-18, with a file datestamp of 2019-12-13.
Experiment type: XRAY
Resolution: 2.21 Å
R-factor: N/A
AEROSPACI score: 0.27 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: ATP-dependent Clp protease proteolytic subunit
    Species: Staphylococcus aureus (strain NCTC 8325) [TaxId:93061]
    Gene: clpP, SAOUHSC_00790
    Database cross-references and differences (RAF-indexed):
  • Chain 'B':
    Compound: ATP-dependent Clp protease proteolytic subunit
    Species: Staphylococcus aureus (strain NCTC 8325) [TaxId:93061]
    Gene: clpP, SAOUHSC_00790
    Database cross-references and differences (RAF-indexed):
  • Chain 'C':
    Compound: ATP-dependent Clp protease proteolytic subunit
    Species: Staphylococcus aureus (strain NCTC 8325) [TaxId:93061]
    Gene: clpP, SAOUHSC_00790
    Database cross-references and differences (RAF-indexed):
  • Chain 'D':
    Compound: ATP-dependent Clp protease proteolytic subunit
    Species: Staphylococcus aureus (strain NCTC 8325) [TaxId:93061]
    Gene: clpP, SAOUHSC_00790
    Database cross-references and differences (RAF-indexed):
  • Chain 'E':
    Compound: ATP-dependent Clp protease proteolytic subunit
    Species: Staphylococcus aureus (strain NCTC 8325) [TaxId:93061]
    Gene: clpP, SAOUHSC_00790
    Database cross-references and differences (RAF-indexed):
  • Chain 'F':
    Compound: ATP-dependent Clp protease proteolytic subunit
    Species: Staphylococcus aureus (strain NCTC 8325) [TaxId:93061]
    Gene: clpP, SAOUHSC_00790
    Database cross-references and differences (RAF-indexed):
  • Chain 'G':
    Compound: ATP-dependent Clp protease proteolytic subunit
    Species: Staphylococcus aureus (strain NCTC 8325) [TaxId:93061]
    Gene: clpP, SAOUHSC_00790
    Database cross-references and differences (RAF-indexed):
  • Chain 'H':
    Compound: SHV-WFP-SER-PRO-YCP-ALA-MP8 Acyldepsipeptide
    Species: synthetic construct, synthetic [TaxId:32630]
    Database cross-references and differences (RAF-indexed):
    • PDB 6PMD (0-6)
  • Chain 'I':
    Compound: ATP-dependent Clp protease proteolytic subunit
    Species: Staphylococcus aureus (strain NCTC 8325) [TaxId:93061]
    Gene: clpP, SAOUHSC_00790
    Database cross-references and differences (RAF-indexed):
  • Chain 'J':
    Compound: SHV-WFP-SER-PRO-YCP-ALA-MP8 Acyldepsipeptide
    Species: synthetic construct, synthetic [TaxId:32630]
    Database cross-references and differences (RAF-indexed):
    • PDB 6PMD (0-6)
  • Chain 'K':
    Compound: ATP-dependent Clp protease proteolytic subunit
    Species: Staphylococcus aureus (strain NCTC 8325) [TaxId:93061]
    Gene: clpP, SAOUHSC_00790
    Database cross-references and differences (RAF-indexed):
  • Chain 'L':
    Compound: ATP-dependent Clp protease proteolytic subunit
    Species: Staphylococcus aureus (strain NCTC 8325) [TaxId:93061]
    Gene: clpP, SAOUHSC_00790
    Database cross-references and differences (RAF-indexed):
  • Chain 'M':
    Compound: ATP-dependent Clp protease proteolytic subunit
    Species: Staphylococcus aureus (strain NCTC 8325) [TaxId:93061]
    Gene: clpP, SAOUHSC_00790
    Database cross-references and differences (RAF-indexed):
  • Chain 'N':
    Compound: ATP-dependent Clp protease proteolytic subunit
    Species: Staphylococcus aureus (strain NCTC 8325) [TaxId:93061]
    Gene: clpP, SAOUHSC_00790
    Database cross-references and differences (RAF-indexed):
  • Chain 'O':
    Compound: SHV-WFP-SER-PRO-YCP-ALA-MP8 Acyldepsipeptide
    Species: synthetic construct, synthetic [TaxId:32630]
    Database cross-references and differences (RAF-indexed):
    • PDB 6PMD (0-6)
  • Chain 'P':
    Compound: SHV-WFP-SER-PRO-YCP-ALA-MP8 Acyldepsipeptide
    Species: synthetic construct, synthetic [TaxId:32630]
    Database cross-references and differences (RAF-indexed):
    • PDB 6PMD (0-6)
  • Chain 'Q':
    Compound: SHV-WFP-SER-PRO-YCP-ALA-MP8 Acyldepsipeptide
    Species: synthetic construct, synthetic [TaxId:32630]
    Database cross-references and differences (RAF-indexed):
    • PDB 6PMD (0-6)
  • Chain 'R':
    Compound: SHV-WFP-SER-PRO-YCP-ALA-MP8 Acyldepsipeptide
    Species: synthetic construct, synthetic [TaxId:32630]
    Database cross-references and differences (RAF-indexed):
    • PDB 6PMD (0-6)
  • Chain 'S':
    Compound: ATP-dependent Clp protease proteolytic subunit
    Species: Staphylococcus aureus (strain NCTC 8325) [TaxId:93061]
    Gene: clpP, SAOUHSC_00790
    Database cross-references and differences (RAF-indexed):
  • Chain 'T':
    Compound: ATP-dependent Clp protease proteolytic subunit
    Species: Staphylococcus aureus (strain NCTC 8325) [TaxId:93061]
    Gene: clpP, SAOUHSC_00790
    Database cross-references and differences (RAF-indexed):
  • Chain 'U':
    Compound: SHV-WFP-SER-PRO-YCP-ALA-MP8 Acyldepsipeptide
    Species: synthetic construct, synthetic [TaxId:32630]
    Database cross-references and differences (RAF-indexed):
    • PDB 6PMD (0-6)
  • Chain 'V':
    Compound: SHV-WFP-SER-PRO-YCP-ALA-MP8 Acyldepsipeptide
    Species: synthetic construct, synthetic [TaxId:32630]
    Database cross-references and differences (RAF-indexed):
    • PDB 6PMD (0-6)
  • Chain 'X':
    Compound: SHV-WFP-SER-PRO-YCP-ALA-MP8 Acyldepsipeptide
    Species: synthetic construct, synthetic [TaxId:32630]
    Database cross-references and differences (RAF-indexed):
    • PDB 6PMD (0-6)
  • Chain 'Y':
    Compound: SHV-WFP-SER-PRO-YCP-ALA-MP8 Acyldepsipeptide
    Species: synthetic construct, synthetic [TaxId:32630]
    Database cross-references and differences (RAF-indexed):
    • PDB 6PMD (0-6)
  • Chain 'Z':
    Compound: SHV-WFP-SER-PRO-YCP-ALA-MP8 Acyldepsipeptide
    Species: synthetic construct, synthetic [TaxId:32630]
    Database cross-references and differences (RAF-indexed):
    • PDB 6PMD (0-6)
  • Heterogens: MPD, HOH

PDB Chain Sequences:
This PDB entry is not classified in SCOPe 2.08, so the chain sequences below are not included in the ASTRAL sequence sets.

  • Chain 'A':
    Sequence, based on SEQRES records:
    >6pmdA (A:)
mnliptviettnrgeraydiysrllkdriimlgsqiddnvansivsqllflqaqdsekdi
ylyinspggsvtagfaiydtiqhikpdvqticigmaasmgsfllaagakgkrfalpnaev
mihqplggaqgqateieiaanhilktreklnrilsertgqsiekiqkdtdrdnfltaeea
keyglidevmvpetklehhhhhh

    Sequence, based on observed residues (ATOM records):
    >6pmdA (A:)
liptviaydiysrllkdriimlgsqiddnvansivsqllflqaqdsekdiylyinspggs
vtagfaiydtiqhikpdvqticigmaasmgsfllaagakgkrfalpnaevmihqplggaq
gqateieiaanhilktreklnrilsertgqsiekiqkdtdrdnfltaeeakeyglidevm
vpet

  • Chain 'B':
    Sequence, based on SEQRES records:
    >6pmdB (B:)
mnliptviettnrgeraydiysrllkdriimlgsqiddnvansivsqllflqaqdsekdi
ylyinspggsvtagfaiydtiqhikpdvqticigmaasmgsfllaagakgkrfalpnaev
mihqplggaqgqateieiaanhilktreklnrilsertgqsiekiqkdtdrdnfltaeea
keyglidevmvpetklehhhhhh

    Sequence, based on observed residues (ATOM records):
    >6pmdB (B:)
iptviraydiysrllkdriimlgsqiddnvansivsqllflqaqdsekdiylyinspggs
vtagfaiydtiqhikpdvqticigmaasmgsfllaagakgkrfalpnaevmihqplggaq
gqateieiaanhilktreklnrilsertgqsiekiqkdtdrdnfltaeeakeyglidevm
vp

  • Chain 'C':
    Sequence, based on SEQRES records:
    >6pmdC (C:)
mnliptviettnrgeraydiysrllkdriimlgsqiddnvansivsqllflqaqdsekdi
ylyinspggsvtagfaiydtiqhikpdvqticigmaasmgsfllaagakgkrfalpnaev
mihqplggaqgqateieiaanhilktreklnrilsertgqsiekiqkdtdrdnfltaeea
keyglidevmvpetklehhhhhh

    Sequence, based on observed residues (ATOM records):
    >6pmdC (C:)
iptviraydiysrllkdriimlgsqiddnvansivsqllflqaqdsekdiylyinspggs
vtagfaiydtiqhikpdvqticigmaasmgsfllaagakgkrfalpnaevmihqplggaq
gqateieiaanhilktreklnrilsertgqsiekiqkdtdrdnfltaeeakeyglidevm
vp

  • Chain 'D':
    Sequence, based on SEQRES records:
    >6pmdD (D:)
mnliptviettnrgeraydiysrllkdriimlgsqiddnvansivsqllflqaqdsekdi
ylyinspggsvtagfaiydtiqhikpdvqticigmaasmgsfllaagakgkrfalpnaev
mihqplggaqgqateieiaanhilktreklnrilsertgqsiekiqkdtdrdnfltaeea
keyglidevmvpetklehhhhhh

    Sequence, based on observed residues (ATOM records):
    >6pmdD (D:)
liptviaydiysrllkdriimlgsqiddnvansivsqllflqaqdsekdiylyinspggs
vtagfaiydtiqhikpdvqticigmaasmgsfllaagakgkrfalpnaevmihqplggaq
gqateieiaanhilktreklnrilsertgqsiekiqkdtdrdnfltaeeakeyglidevm
vp

  • Chain 'E':
    Sequence, based on SEQRES records:
    >6pmdE (E:)
mnliptviettnrgeraydiysrllkdriimlgsqiddnvansivsqllflqaqdsekdi
ylyinspggsvtagfaiydtiqhikpdvqticigmaasmgsfllaagakgkrfalpnaev
mihqplggaqgqateieiaanhilktreklnrilsertgqsiekiqkdtdrdnfltaeea
keyglidevmvpetklehhhhhh

    Sequence, based on observed residues (ATOM records):
    >6pmdE (E:)
liptviydiysrllkdriimlgsqiddnvansivsqllflqaqdsekdiylyinspggsv
tagfaiydtiqhikpdvqticigmaasmgsfllaagakgkrfalpnaevmihqplggaqg
qateieiaanhilktreklnrilsertgqsiekiqkdtdrdnfltaeeakeyglidevmv
pe

  • Chain 'F':
    Sequence, based on SEQRES records:
    >6pmdF (F:)
mnliptviettnrgeraydiysrllkdriimlgsqiddnvansivsqllflqaqdsekdi
ylyinspggsvtagfaiydtiqhikpdvqticigmaasmgsfllaagakgkrfalpnaev
mihqplggaqgqateieiaanhilktreklnrilsertgqsiekiqkdtdrdnfltaeea
keyglidevmvpetklehhhhhh

    Sequence, based on observed residues (ATOM records):
    >6pmdF (F:)
liptviydiysrllkdriimlgsqiddnvansivsqllflqaqdsekdiylyinspggsv
tagfaiydtiqhikpdvqticigmaasmgsfllaagakgkrfalpnaevmihqplggaqg
qateieiaanhilktreklnrilsertgqsiekiqkdtdrdnfltaeeakeyglidevmv
p

  • Chain 'G':
    Sequence, based on SEQRES records:
    >6pmdG (G:)
mnliptviettnrgeraydiysrllkdriimlgsqiddnvansivsqllflqaqdsekdi
ylyinspggsvtagfaiydtiqhikpdvqticigmaasmgsfllaagakgkrfalpnaev
mihqplggaqgqateieiaanhilktreklnrilsertgqsiekiqkdtdrdnfltaeea
keyglidevmvpetklehhhhhh

    Sequence, based on observed residues (ATOM records):
    >6pmdG (G:)
liptviydiysrllkdriimlgsqiddnvansivsqllflqaqdsekdiylyinspggsv
tagfaiydtiqhikpdvqticigmaasmgsfllaagakgkrfalpnaevmihqplggaqg
qateieiaanhilktreklnrilsertgqsiekiqkdtdrdnfltaeeakeyglidevmv
p

  • Chain 'H':
    Sequence; same for both SEQRES and ATOM records:
    >6pmdH (H:)
xxspxax

  • Chain 'I':
    Sequence, based on SEQRES records:
    >6pmdI (I:)
mnliptviettnrgeraydiysrllkdriimlgsqiddnvansivsqllflqaqdsekdi
ylyinspggsvtagfaiydtiqhikpdvqticigmaasmgsfllaagakgkrfalpnaev
mihqplggaqgqateieiaanhilktreklnrilsertgqsiekiqkdtdrdnfltaeea
keyglidevmvpetklehhhhhh

    Sequence, based on observed residues (ATOM records):
    >6pmdI (I:)
liptviaydiysrllkdriimlgsqiddnvansivsqllflqaqdsekdiylyinspggs
vtagfaiydtiqhikpdvqticigmaasmgsfllaagakgkrfalpnaevmihqplggaq
gqateieiaanhilktreklnrilsertgqsiekiqkdtdrdnfltaeeakeyglidevm
vpe

  • Chain 'J':
    Sequence; same for both SEQRES and ATOM records:
    >6pmdJ (J:)
xxspxax

  • Chain 'K':
    Sequence, based on SEQRES records:
    >6pmdK (K:)
mnliptviettnrgeraydiysrllkdriimlgsqiddnvansivsqllflqaqdsekdi
ylyinspggsvtagfaiydtiqhikpdvqticigmaasmgsfllaagakgkrfalpnaev
mihqplggaqgqateieiaanhilktreklnrilsertgqsiekiqkdtdrdnfltaeea
keyglidevmvpetklehhhhhh

    Sequence, based on observed residues (ATOM records):
    >6pmdK (K:)
liptviraydiysrllkdriimlgsqiddnvansivsqllflqaqdsekdiylyinspgg
svtagfaiydtiqhikpdvqticigmaasmgsfllaagakgkrfalpnaevmihqplgga
qgqateieiaanhilktreklnrilsertgqsiekiqkdtdrdnfltaeeakeyglidev
mvp

  • Chain 'L':
    Sequence, based on SEQRES records:
    >6pmdL (L:)
mnliptviettnrgeraydiysrllkdriimlgsqiddnvansivsqllflqaqdsekdi
ylyinspggsvtagfaiydtiqhikpdvqticigmaasmgsfllaagakgkrfalpnaev
mihqplggaqgqateieiaanhilktreklnrilsertgqsiekiqkdtdrdnfltaeea
keyglidevmvpetklehhhhhh

    Sequence, based on observed residues (ATOM records):
    >6pmdL (L:)
iptviraydiysrllkdriimlgsqiddnvansivsqllflqaqdsekdiylyinspggs
vtagfaiydtiqhikpdvqticigmaasmgsfllaagakgkrfalpnaevmihqplggaq
gqateieiaanhilktreklnrilsertgqsiekiqkdtdrdnfltaeeakeyglidevm
vp

  • Chain 'M':
    Sequence, based on SEQRES records:
    >6pmdM (M:)
mnliptviettnrgeraydiysrllkdriimlgsqiddnvansivsqllflqaqdsekdi
ylyinspggsvtagfaiydtiqhikpdvqticigmaasmgsfllaagakgkrfalpnaev
mihqplggaqgqateieiaanhilktreklnrilsertgqsiekiqkdtdrdnfltaeea
keyglidevmvpetklehhhhhh

    Sequence, based on observed residues (ATOM records):
    >6pmdM (M:)
liptvydiysrllkdriimlgsqiddnvansivsqllflqaqdsekdiylyinspggsvt
agfaiydtiqhikpdvqticigmaasmgsfllaagakgkrfalpnaevmihqplggaqgq
ateieiaanhilktreklnrilsertgqsiekiqkdtdrdnfltaeeakeyglidevmvp
e

  • Chain 'N':
    Sequence, based on SEQRES records:
    >6pmdN (N:)
mnliptviettnrgeraydiysrllkdriimlgsqiddnvansivsqllflqaqdsekdi
ylyinspggsvtagfaiydtiqhikpdvqticigmaasmgsfllaagakgkrfalpnaev
mihqplggaqgqateieiaanhilktreklnrilsertgqsiekiqkdtdrdnfltaeea
keyglidevmvpetklehhhhhh

    Sequence, based on observed residues (ATOM records):
    >6pmdN (N:)
liptviydiysrllkdriimlgsqiddnvansivsqllflqaqdsekdiylyinspggsv
tagfaiydtiqhikpdvqticigmaasmgsfllaagakgkrfalpnaevmihqplggaqg
qateieiaanhilktreklnrilsertgqsiekiqkdtdrdnfltaeeakeyglidevmv
pe

  • Chain 'O':
    Sequence; same for both SEQRES and ATOM records:
    >6pmdO (O:)
xxspxax

  • Chain 'P':
    Sequence; same for both SEQRES and ATOM records:
    >6pmdP (P:)
xxspxax

  • Chain 'Q':
    Sequence; same for both SEQRES and ATOM records:
    >6pmdQ (Q:)
xxspxax

  • Chain 'R':
    Sequence; same for both SEQRES and ATOM records:
    >6pmdR (R:)
xxspxax

  • Chain 'S':
    Sequence, based on SEQRES records:
    >6pmdS (S:)
mnliptviettnrgeraydiysrllkdriimlgsqiddnvansivsqllflqaqdsekdi
ylyinspggsvtagfaiydtiqhikpdvqticigmaasmgsfllaagakgkrfalpnaev
mihqplggaqgqateieiaanhilktreklnrilsertgqsiekiqkdtdrdnfltaeea
keyglidevmvpetklehhhhhh

    Sequence, based on observed residues (ATOM records):
    >6pmdS (S:)
liptviaydiysrllkdriimlgsqiddnvansivsqllflqaqdsekdiylyinspggs
vtagfaiydtiqhikpdvqticigmaasmgsfllaagakgkrfalpnaevmihqplggaq
gqateieiaanhilktreklnrilsertgqsiekiqkdtdrdnfltaeeakeyglidevm
vp

  • Chain 'T':
    Sequence, based on SEQRES records:
    >6pmdT (T:)
mnliptviettnrgeraydiysrllkdriimlgsqiddnvansivsqllflqaqdsekdi
ylyinspggsvtagfaiydtiqhikpdvqticigmaasmgsfllaagakgkrfalpnaev
mihqplggaqgqateieiaanhilktreklnrilsertgqsiekiqkdtdrdnfltaeea
keyglidevmvpetklehhhhhh

    Sequence, based on observed residues (ATOM records):
    >6pmdT (T:)
liptvydiysrllkdriimlgsqiddnvansivsqllflqaqdsekdiylyinspggsvt
agfaiydtiqhikpdvqticigmaasmgsfllaagakgkrfalpnaevmihqplggaqgq
ateieiaanhilktreklnrilsertgqsiekiqkdtdrdnfltaeeakeyglidevmvp
e

  • Chain 'U':
    Sequence; same for both SEQRES and ATOM records:
    >6pmdU (U:)
xxspxax

  • Chain 'V':
    Sequence; same for both SEQRES and ATOM records:
    >6pmdV (V:)
xxspxax

  • Chain 'X':
    Sequence; same for both SEQRES and ATOM records:
    >6pmdX (X:)
xxspxax

  • Chain 'Y':
    Sequence; same for both SEQRES and ATOM records:
    >6pmdY (Y:)
xxspxax

  • Chain 'Z':
    Sequence; same for both SEQRES and ATOM records:
    >6pmdZ (Z:)
xxspxax